The mission code seems to be changing quite a lot recently. Some of what is in this post might be updated by now. This is stuff I've noticed over the last couple of months.

From 1.7 and 1.8a1

In general a lot of the missions tell you what the target is before you undock but it comes up as "Unknown Friendly" or "Unknown Hostile" on the directional indicator. Settting the target as known would be more consistent since we already know, for example, that we will be destroying a Charon Pirate Cache or going to Asteroid 512754.
Seen in Benedict Eridani missions, mining missions, Fleet missions taking supplies to a station.

Korolov missions
The "escort the incoming freighter from the stargate" Korolov mission also comes up as "Unknown friendly". Having the stargate name as the target until the freighter arrives would be better, like in the Fleet refugee escort missions.

The "Destroy the Charon Stronghold" missions in Korolov stations can be a long, long way away. 55 and 41 light minutes are recent game examples. A bit closer would work. Some are off the system map grid!

The 1.8a1 "Do you want an escort mission" screen is redundant. Changing the actual accept/decline screen is preferable to having an extra screen which does nothing except continue on to the accept/decline screen.

Rigel Black Market mission
The directional indicator targets the station not the Molotok that is meant to be destroyed. Confusing.

You can also dock at the destroyed BM station before Kate gets there and talk to her. Maybe a "You decide to wait for Kate" screen could be included.

Fleet missions
Rescue Scientists
The station is dead and "No one is left alive" before the Aurochs docks. Seems odd.

Refugee Escort
All the Centurions were killed, 3 Scarabs and 2 EI100 gated out successfully but still got the "You screwed up the mission" screen.
Next time; 4 Centurions killed and the mission was over and the refugee ships never appeared. Is the mission outcome dependent on Centurion lives? That doesn't seem right.

Mining missions
It's probably worthwhile changing the scrDesc in the Borer rescue mission to include that the ship now needs to be escorted back to the station to complete the mission. In previous versions it was OK to leave the ship out there to die.

Ag station mission
Seen in 1.7. On mission completion the ship is undocked rather than returning to the main station dockscreen.

The new missions are great. A lot of the oddities and bugs have been fixed and they run a lot smoother. Well done to all involved.

Antarctica suggestions 1.8a3
Without orders from Decker. ie, you find the Antarctica first.

The action "Yes - He says you betrayed the fleet" probably shouldn't come up given that the player hasn't spoken to Decker.

On selecting "I have no idea what you're talking about" the briefing continues via textBriefing2b.
However when you get to textBriefing4 you get two actions."I won't try to stop you" and "I have my orders".
Given the player has no orders the second action could be changed to "Gonna kill ya coz you're a traitor" or preferably something a bit more polished .

Separately;
If you help the Antarctica, after destroying the Aquilas the CSC could be highlighted as a destination so the player knows to dock and collect the gift.

CSC Fleet missions 1.8a3
Not a game breaker, but the CSC America had me do a visual recon on the same Ares Commune twice in a row. Seemed odd.
Suggestion: Only have one recon per station or modify the mission screen desc to say "another" recon.

These seem to be related to msKorolovAtCharon in KSMissionC01.xml. The ship classes are Ronin A and B and EI200. The orders are guard and dock. So the first set of errors are probably from the OnGlobalSystemStarted event, but I don't see why it wouldn't work. The other error is in the OnTimerAttack2 event, probably if the Korolov station was destroyed before the second wave spawns or the player isn't in Charon anymore.

tbCommPrivateCraft has a gateOnThreat order on the end instead of guard.

Every other use of these tables is in a StationType UNID <Ships> or <Reinforcements> block so the default target for the order is assumed as the station that is being created (I'm guessing here but it seems to fit).

Creating the ship in a MissionType UNID means the code can't find a default station type to 'assume' as the order target.

So I suspect the tbCommDefender ships can't do shipOrder 1 which is the guard order in the table because there is no target for it to guard.

The tbCommPrivateCraft ship can do the inbuilt table order, gateOnThreat, because it doesn't need a target. Checking the ship orders on the private craft shows a gateOnThreat order then the dock order then the second gateOnThreat order.
Not sure why it is saying "Unable to add ship order 2" though. It is able to do it. Unless ship order is something different in debugging.

Overwriting the tables to remove the orders fixes everything. No errors appear in the debug log and the only orders are the ones added in the mission code.

Mining missions used to show the 'Welcome to 'station name', saw your ship on the display' screen description for the first mission from that station. For any further missions the screen description was "We have another mission for you" or similar.

In 1.8b3.3 and 1.8b4 the only mission intro screen I've seen is the first one, 'Welcome to 'station name', saw your ship on the display'.
Possibly a regression?

Although the CSC Antarctica launches patrols every so often it doesn't launch any ships if the player says they will attack it. Having half a dozen Centurions pop out and attack the player as they undock might make it exciting. No idea if this idea is balanced though. I haven't fought the Antarctica when equipped with normal weapons in quite some time.